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Illumina
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18
votes
37
replies
17k
views
Correct construction of design matrix in limma for multiple contrasts for gene expression profiling
limma
illumina
differential gene expression
multiple comparisons
design matrix
8.9 years ago • updated 8.8 years ago
svlachavas
▴ 830
4
votes
8
replies
10k
views
how to use idat file for analyses in bioconductor
microarray
illumina
idat
updated 8.2 years ago by
Gordon Smyth
50k • written 8.2 years ago by
kritikamish99
▴ 10
1
vote
7
replies
5.9k
views
convert fastq file to fasta using shortread package
illumina
shortread
updated 9.1 years ago by
Martin Morgan
25k • written 9.1 years ago by
kelvinfrog75
• 0
0
votes
2
replies
5.3k
views
How to read bgx files in R
microarray
annotation
illumina
8.8 years ago
kanacska
▴ 10
4
votes
2
replies
4.6k
views
gene annotation of Illumina HumanWG-6 v3.0 expression beadchip
illumina
updated 9.5 years ago by
James W. MacDonald
65k • written 9.5 years ago by
Li Liu
▴ 100
3
votes
15
replies
4.4k
views
Installing MethylationEPIC minifest and annotation
minfi
methylation
illuminahumanmethylationepicmanifest
illumina
8.1 years ago
rasii
• 0
0
votes
6
replies
4.0k
views
How to normalize in R Illumina HumanHT-12 V3.0 expression beadchip data
illumina
normalization
microarray
updated 8.8 years ago by
Mark Dunning
★ 1.1k • written 8.8 years ago by
kanacska
▴ 10
1
vote
14
replies
3.7k
views
GWAS analysis with Illumina HumanOmni5-4 BeadChip - recommended software and workflow
GWASTools
qualitycontrol
HumanOmni5-4BeadChip
GenomeStudio
illumina
updated 8.0 years ago by
Stephanie M. Gogarten
▴ 870 • written 8.0 years ago by
Lna
• 0
4
votes
5
replies
2.9k
views
Is it sensable to use p-value detection in illumina bead array as present, absent or marginal call
illumina
pvalue
updated 8.9 years ago by
svlachavas
▴ 830 • written 8.9 years ago by
Agaz Hussain Wani
▴ 260
2
votes
3
replies
2.5k
views
Normalization of Illumina Microarray Data
illumina
microarray
normalization
updated 7.2 years ago by
Gordon Smyth
50k • written 7.2 years ago by
paul.elliot1994
• 0
0
votes
0
replies
2.5k
views
lumiR error Error in gregexpr("\t", dataLine1)[[1]] : subscript out of bounds
lumi
illumina
normalization
beadarray
7.0 years ago
hkarakurt
▴ 20
3
votes
6
replies
2.4k
views
How to get a list of differentialy expressed genes with data from Illumina array?
limma
illumina
microarray
lmfit
differential gene expression
updated 8.8 years ago by
James W. MacDonald
65k • written 8.8 years ago by
kanacska
▴ 10
0
votes
4
replies
2.4k
views
Illumina Sentrix HumanRef-8 Expression BeadChip annotation file
illumina
annotation
updated 8.6 years ago by
Mike Smith
★ 6.5k • written 8.6 years ago by
kanacska
▴ 10
11
votes
5
replies
2.3k
views
Why is the "detection" value given by lumidat the inverse (i.e. 1-x) of the "detection_pval" given by GenomeStudio?
lumidat
idat
microarray
illumina
updated 8.6 years ago by
Mark Cowley
▴ 400 • written 8.6 years ago by
willj
▴ 30
2
votes
5
replies
2.3k
views
Errors in Processing GSE36411_non-normalized.txt file of Illumina data using lumi Package and limma package
limma
lumi
illumina
gene expression data
updated 2.4 years ago by
mohammedtoufiq91
▴ 10 • written 5.9 years ago by
Harpreet Kaur
• 0
0
votes
6
replies
2.2k
views
Illumina bead array analysis
illumina
beadarray
updated 14 months ago by
Mark Dunning
★ 1.1k • written 9.6 years ago by
tomiptu
• 0
0
votes
3
replies
2.2k
views
neqc normalization results in bimodal histogram of expression values
neqc
limma
microarray
illumina
updated 8.2 years ago by
Gordon Smyth
50k • written 8.2 years ago by
alexvpickering
▴ 110
0
votes
1
reply
2.1k
views
Question about neqc and GEO illumina files
neqc
illumina
geo
limma
updated 7.9 years ago by
Gordon Smyth
50k • written 7.9 years ago by
akridgerunner
▴ 30
1
vote
6
replies
2.1k
views
Copy number analysis from Illumina 550K chip
illumina
copynumber
crlmm
8.5 years ago
stuti.agrawal
• 0
0
votes
7
replies
2.0k
views
Annotation of probes from Affymetrix and Illumina platforms in MACQ project ?
Affymetrix
Illumina
probes
microarray
annotation package
updated 5.0 years ago by
Guido Hooiveld
★ 3.9k • written 5.0 years ago by
naf
• 0
0
votes
2
replies
1.9k
views
Help resovling"Error in lm.fit" with 'dmpFinder' function in minfi
minfi
minfidata
illumina
methylation
dmpfinder
updated 9.6 years ago by
James W. MacDonald
65k • written 9.6 years ago by
michael.zulyniak
• 0
1
vote
5
replies
1.9k
views
CRLMM on Illumina Human1Mv1_C chips
crlmm
illumina
beadarraysnp
updated 9.2 years ago by
Matthew Ritchie
▴ 1000 • written 9.2 years ago by
René
▴ 30
0
votes
3
replies
1.9k
views
Error and warning message when reading the ballgown object
software error
illumina
DEG
ballgown
tuxedo
updated 6.1 years ago by
James W. MacDonald
65k • written 6.1 years ago by
amy16
• 0
0
votes
4
replies
1.9k
views
Aclust package: IlluminaHumanMethylation450kCHR37 not found
illuminahumanmethylation450k.db
aclust
methylation
annotation
illumina
updated 7.6 years ago by
b2cemaillist
• 0 • written 7.7 years ago by
aagata.szymanek
• 0
0
votes
2
replies
1.9k
views
Illumina methylationEPIC demo data in IDAT format?
methylation
illumina
EPIC
methylationepic
idat
updated 7.0 years ago by
Guido Hooiveld
★ 3.9k • written 7.0 years ago by
Ellen O
• 0
0
votes
2
replies
1.8k
views
Reading IDAT files from Illumina HumanMethylation450 BeadChip with beadarray
beadarray
illumina
methylation
microarray
updated 8.6 years ago by
Sean Davis
21k • written 8.6 years ago by
maria.keays
• 0
1
vote
4
replies
1.8k
views
Trouble loading 'lumi' package
lumi
illumina
hdf5array
updated 5.7 years ago by
James W. MacDonald
65k • written 5.7 years ago by
Alexander Azarian
▴ 30
0
votes
0
replies
1.8k
views
Any alternative to GenomeStudio to analyze Illumina VeraCode arrays? Is Beadarray an option?
microarray
beadarray
Illumina
Veracode
9.3 years ago
lacion
• 0
1
vote
1
reply
1.7k
views
How to convert Illumina HumanMethylation27 BeadChip ID's to gene names?
gene names
methylation
illumina
convertids
updated 6.0 years ago by
James W. MacDonald
65k • written 6.0 years ago by
arbet003
▴ 10
0
votes
7
replies
1.6k
views
getting error in processSwathData command from the beadarray package
microarray
beadarray
illumina
updated 9.1 years ago by
Mike Smith
★ 6.5k • written 9.1 years ago by
harpreet.saini
• 0
2
votes
4
replies
1.6k
views
read.idat function misleading error when reading compressed files
idat
illumina
limma
read.idat
updated 3.4 years ago by
Gordon Smyth
50k • written 3.4 years ago by
bastien_chassagnol
• 0
7
votes
4
replies
1.6k
views
very high adjusted P-vals using Illumina data from GEO
limma
p values
microarray
illumina
updated 8.3 years ago by
James W. MacDonald
65k • written 8.3 years ago by
Jason
▴ 20
0
votes
1
reply
1.6k
views
Error regarding installation and loading of "Lumi" Package
software error
microarray
illumina
updated 9.3 years ago by
Steve Lianoglou
★ 13k • written 9.3 years ago by
Deeksha Malhan
▴ 10
2
votes
2
replies
1.6k
views
Annotation problems regarding quality information for Illumina HumanHT-12 v4-illuminaHumanv4.db
illumina human ht-12 v4
illuminahumanv4.db
filtering on probe annotation
illumina
updated 8.9 years ago by
Mike Smith
★ 6.5k • written 8.9 years ago by
svlachavas
▴ 830
0
votes
3
replies
1.6k
views
MINFI missing samples in qcreports and densityplots
minfi
illumina
methylationEPIC
densityplot
7.3 years ago
annabelle.congras
▴ 10
2
votes
3
replies
1.6k
views
lumiR [Illumina] error from non-normalized data
illumina
updated 7.7 years ago by
Gordon Smyth
50k • written 7.7 years ago by
Stane
▴ 40
0
votes
4
replies
1.6k
views
minfi sample limit
minfi
illumina
illimina 450k methylation
methylation
updated 8.1 years ago by
Kasper Daniel Hansen
★ 6.5k • written 8.1 years ago by
igor
▴ 40
6
votes
9
replies
1.6k
views
Interpretation of DE analysis results of an Illumina microarray dataset, and possible batch effect size problem
limma
illumina
microarray
multifactorial design
batch effect
updated 7.9 years ago by
Gordon Smyth
50k • written 7.9 years ago by
Konstantinos Yeles
▴ 80
0
votes
1
reply
1.5k
views
Error in Matrix
minfi
methylation
EPIC microarray
illumina
updated 8.0 years ago by
Kasper Daniel Hansen
★ 6.5k • written 8.0 years ago by
rasii
• 0
0
votes
3
replies
1.5k
views
How can I pre-process illumina raw file
illumina
microarray
updated 6.7 years ago by
James W. MacDonald
65k • written 6.7 years ago by
Agaz Hussain Wani
▴ 260
1
vote
2
replies
1.5k
views
minfi package QC report error?
minfi
methylation
illumina
9.5 years ago
Brian Smith
▴ 120
0
votes
0
replies
1.5k
views
Issue with finding .idat files when analysing illumina methylation microarrays using RnBeads
rnbeads
methylation
illumina
epic microarray
7.7 years ago
rasii
• 0
2
votes
1
reply
1.5k
views
Normalization and background correction issues for specific Illumina data sets using limma R package
illumina
bioconductor
limma
microarray
normalization
updated 8.5 years ago by
Gordon Smyth
50k • written 8.5 years ago by
Konstantinos Yeles
▴ 80
1
vote
3
replies
1.5k
views
Minfi returning incorrect beta values
minfi
illumina
illumina450k
methylation
R
6.8 years ago
ezrabekele17
• 0
2
votes
1
reply
1.4k
views
Differential Expression Analysis
differential gene expression
microarray
lumi
illumina
updated 7.1 years ago by
James W. MacDonald
65k • written 7.1 years ago by
paul.elliot1994
• 0
1
vote
1
reply
1.4k
views
Illumina Infinium Global Screening Array (GSA) v1.0 for CRLMM
crlmm
gsa
microarray
illumina
written 6.0 years ago by
shaun
• 0
0
votes
0
replies
1.4k
views
minfi v1.14 through champ: read.450k error with file path name
minfi
champ
illumina
450k
8.7 years ago
jeroen
• 0
0
votes
0
replies
1.4k
views
How can I do paired test on my Illumina 450k idat files with ChAMP package?
Illumina
450k
ChAMP
paired test
8.2 years ago
walter_teng
• 0
1
vote
1
reply
1.4k
views
RNA-seq for DGE
stringtie
illumina
hisat2
ballgown
updated 6.5 years ago by
k.vitting.seerup
▴ 120 • written 6.5 years ago by
amy16
• 0
1
vote
2
replies
1.4k
views
Methylation data visualization using methyAnalysis with minfi
methylation
microarray
illumina
minfi
methyanalysis
updated 5.4 years ago by
Ou, Jianhong
★ 1.3k • written 5.4 years ago by
Adam_M
• 0
50 results • Page
1 of 1
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Replies
Answer: Once again a "Model matrix not full rank"
by
swbarnes2
★ 1.3k
Replicate numbers, like the 1 in control_1 are fine in sample names, but never add them to anything else in colData. From the computer's p…
Answer: limma Intercept vs No-intercept models completely changing DMR results?
by
Gordon Smyth
50k
I'll add a little bit of general advice to James' answer. You seem to have the misunderstanding that you can change the design matrix but …
Answer: package goseq seems to be not available on the latest version of R
by
Gordon Smyth
50k
It is true that goseq isn't available for Bioc 3.19. That is because goseq depends on txbmaker, which is itself not yet available for Bioc…
Answer: limma Intercept vs No-intercept models completely changing DMR results?
by
James W. MacDonald
65k
This part: ``` design_intercept <- model.matrix(~Alt+Sex+Age+PC1, data=targets_Sherpa) colnames(design_intercept) <- c("AltSHP_LA","Al…
Comment: CombineArrays for EPIC and EPIC V2
by
Kim
• 0
Thank you Tim, this is a great help in getting me started!
Votes
Answer: limma Intercept vs No-intercept models completely changing DMR results?
Answer: CombineArrays for EPIC and EPIC V2
Answer: Too many significant genes when integrating gtex and tcga
Comment: Too many significant genes when integrating gtex and tcga
A: Print Differentially Expressed Exons From Dexseq Results
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